Fletcher struck from the edge of the box with a right-footed drive in the first of five minutes of stoppage time after his side had been pegged back having led 2-0.
Delighted Mariner hailed his captain, saying: "I don't like to single players out but that was a very important goal and it was a lot more difficult to score than it looked.
"It was under his body when the ball broke to him and yet he has drilled it right into the corner of the goal. It was a brilliant finish and worthy of winning any match - and you could see how much it meant to him."
Mariner added: "To be perfectly honest I am tired but absolutely delighted. Obviously the win was important and to be two ahead at half-time through two quality goals was important but I knew that Gary (Johnson) would have them fired up for the second half and that proved to be the case.
"It was great to get the win and we will let that sink in tonight before we start looking ahead to going to Scunthorpe on Saturday.
"Scunthorpe have a difficult game at Newcastle on Wednesday night but we just look at what we are doing - and that's what we concentrate on."
The Pilgrims looked on course for a straightforward three points when Chris Clark netted his first league goal for the club before Bradley Wright-Phillips doubled the advantage before the break.
Nicky Maynard grabbed his first goals of 2010 to level matters, but Jamal Campbell-Ryce was dismissed for a second bookable offence late on.
And Argyle had the final say as Fletcher fired home a right-footed shot from 20 yards in the final minute.
Johnson rued: "It was a soul destroying way to lose really, especially after we had got back into it. We have done it again and given away another late goal but we didn't start that well, so that was disappointing.
"We came out fighting in the second half and gave it a bit of a go and the momentum was with us, we got it to 2-2 but in the end we have lost three points.
"Nicky got his two terrific goals with two great strikes - one from a free-kick we have worked on and another from open play
- so that's a good sign that he's got a couple but we need to be better than we were in the first half.
"We sent them out a lot more aggressive in the second half and they responded."